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BioC 3.2: CHECK report for GGBase on zin1

This page was generated on 2015-08-24 10:47:30 -0700 (Mon, 24 Aug 2015).

Package 425/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGBase 3.31.2
VJ Carey
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGBase
Last Changed Rev: 105567 / Revision: 107696
Last Changed Date: 2015-06-27 08:03:48 -0700 (Sat, 27 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GGBase
Version: 3.31.2
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GGBase_3.31.2.tar.gz
StartedAt: 2015-08-24 00:18:59 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:21:44 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 165.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GGBase.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GGBase_3.31.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GGBase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGBase/DESCRIPTION’ ... OK
* this is package ‘GGBase’ version ‘3.31.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GGBase’ can be installed ... [12s/12s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘stats::IQR’ when loading ‘GGBase’
See ‘/home/biocbuild/bbs-3.2-bioc/meat/GGBase.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘snpStats’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘MAFfilter.R’ [10s/10s]
  Running ‘make.R’ [10s/10s]
  Running ‘plot_EvG.R’ [11s/11s]
 [31s/31s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/GGBase.Rcheck/00check.log’
for details.


GGBase.Rcheck/00install.out:

* installing *source* package ‘GGBase’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘stats::IQR’ when loading ‘GGBase’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘stats::IQR’ when loading ‘GGBase’
* DONE (GGBase)

GGBase.Rcheck/GGBase-Ex.timings:

nameusersystemelapsed
MAFfilter3.6250.0723.851
clipPCs0.0010.0000.000
externalize000
make_smlSet3.1690.0283.194
plot_EvG3.4260.0283.467
rsid-class0.0020.0000.002
smlSet-class0.0000.0040.001